title: PCOS  decidualised endometrial stromal cells present with altered effects of androgens

city: Tartu

first: Alvin

last: Meltsov

state: Tartumaa

address: Teaduspargi tn 13

country: Estonia

institute: The Competence Centre on Health Technologies

summary: The goal of the study was to assess transcriptome profile of non-decidualized (non-DE) and decidualized (DE) endometrial stromal cells (eSCs) obtained from women with polycystic ovary syndrome (PCOS, eSCPCOS) and non-PCOS controls (eSCCtrl) in response to short-term estradiol (E2) and/or progesterone (P4) exposure with or without dihydrotestosterone (DHT). The eSCs used for RNA-sequencing (RNA-seq) were isolated from proliferative stage endometrium from women with PCOS (diagnosed based on Rotterdam criteria) and non-PCOS controls (n=6 per group). The same eSCs were used for in vitro validation by immunofluorescence (IF; n=3/group). Tissue validation by immunohistochemistry (IHC) was done using whole biopsy formalin-fixed proliferative (PE) and secretory phase (SE) endometrial samples (IHC; n=6/cycle phase/group). Our data provided the observation that Decidualized eSCPCOS display a distinct transcriptome profile, especially in the presence of DHT.

overall_design: DE eSCs (0.5 mM 8-Br-cAMP, 96 h), as model of SE, were treated with E2 and P4 (E2P4) with/without (±) DHT; while non-DE eSCs, as model of PE, were subjected to E2 ± DHT (post-treatment). The 24-hour steroid hormone exposure was followed by RNA-seq.

first: Masuma

last: Khatun

first: Andres

last: Salumets

first: Terhi

middle: T

last: Piltonen


title: Proprotein Convertase Subtilisin/kexin Type 9 is required for Ahnak-mediated Metastasis of Melanoma into Lung Epithelial Cells.

status: Public on Aug 18 2021

city: Seoul

first: Ye Lin

last: Son

state: Seoul

address: Ewha womans university Science Building C 5th floor

country: South Korea

institute: Ewha womans university

type: Expression profiling by high throughput sequencing

summary: Previously we demonstrated that Ahnak mediated transforming growth factor-β (TGFβ)-induced epithelial-mesenchymal transition (EMT) during tumor metastasis. It is well-known that circulating tumor cells (CTCs) invade the vasculature of adjacent target tissues before working to adapt to the host environments. Currently, the molecular mechanism by which infiltrated tumor cells interact with host cells to survive within target tissue environments is far from clear. Here, we show that Ahnak regulates tumor metastasis through PCSK9 expression. To validate the molecular function of Ahnak in metastasis, wild-type (WT) B16F10 melanoma cells were injected into WT and Ahnak knockout (Ahnak-/-) mice. Ahnak-/- mice were more resistant to the pulmonary metastasis of B16F10 cells compared to WT mice. To investigate the host function of Ahnak in recipient organs against metastasis of melanoma cells, transcriptomic analyses of primary pulmonary endothelial cells from WT or Ahnak-/- mice in the absence or presence of TGFβ stimulation were performed. We found PCSK9, along with several other candidate genes, was involved in the invasion of melanoma cells into lung tissues. PCSK9 expression in the pulmonary artery was higher in WT mice than Ahnak-/- mice. To evaluate the host function of PCSK9 in lung tissues during the metastasis of melanoma cells, we established lung epithelial cell-specific tamoxifen-induced PCSK9 conditional KO mice (Scgb1-Cre/PCSK9fl/fl). The pulmonary metastasis of B16F10 cells in Scgb1-Cre/PCSK9fl/fl mice was significantly suppressed, indicating that PCSK9 plays an important role in the metastasis of melanoma cells. Taken together, our data demonstrate that Ahnak regulates metastatic colonization through the regulation of PCSK9 expression.

overall_design: RNA sequencing data from primary pulmonary endothelial cells (ECs) harvested from WT and Ahnak-/- mice in the absence or presence of TGFβ stimulation.

first: Jung

middle: M

last: Suh

first: Yelin

first: Jung-Yeon

last: Yoo

first: Yookyung

last: Goh

first: Nabil

middle: G

last: Seidah

first: Sanghyuk

last: Lee

first: Yun

middle: S

last: Bae


title: Ascoviruses radically optimize virion proliferation by fully cleaving host cells into viral vesicles that circulate in hemolymph

city: Pomona

first: Peter

last: Arensburger

state: CA

address: 3801 Watkins Avenue

department: Dept. of Biology

country: USA

institute: California State Polytechnic University Pomona

summary: We used RNA-Sequencing technology to analyze the transcriptomes of two ascovirus isolates, SfAV and TnAV, over three weeks.

sample_organism:
Spodoptera frugiperda
Trichoplusia ni

platform_organism:
Spodoptera frugiperda
Trichoplusia ni

overall_design: Spodopetera frugiperda and Trichoplusia ni were infected with one of two ascoviruses, SfAV or TnAV respectively, and host tissue samples were sequenced with RNA-Sequencing technology over time in three replicates.

first: Heba

middle: A

last: Zaghloul

first: Robert

middle: H

last: Hice

first: Dennis

middle: K

last: Bideshi

first: Brian

last: Federici


title: Expression data from two thyroid cell lines following miR-7-5p or negative control transfection

city: Bruxelles

first: Alice

last: Augenlicht

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary:
miR-7-5p is a recently discovered downregulated miRNA in thyroid papillary carcinoma (PTC).
The goal of this project was to characterize the role of miR-7-5p in thyroid tumorigenesis and to identify the targeted modulated pathways.

overall_design: miR-7-5p was transiently transfected into TPC1 and HT-ori3 cells, two thyroid-derived cell lines, in order to perform functional assays and to study global gene expression. Functional assays, RNA extraction and hybridization on Affymetrix microarrays are performed 4 days after transfection.

first: Carine

last: Maenhaut


title: Transcriptomics in rabbit bleb after trabeculectomy

city: Kumamoto

first: Tomokazu

last: Fujimoto

address: 1-1-1 Honjo

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

summary: We investigated the roles of IL-6 family members during the wound healing process after trabeculectomy (TL). At the surgical site, the expression levels of genes encoding IL-6, oncostatin M, their receptors, and collagen I were elevated at 3 hours after TL, whereas the levels of genes encoding TGF-β, α-SMA, type IV collagen, and fibronectin were elevated at 3 days after TL.

overall_design: Conjunctival mRNA profiles of trabeclectomy operated and normal rabbit eye

first: Fumika

last: Watanabe

first: Toshihiro

last: Inoue


title: Human bronchial epithelial cell-derived extracellular vesicles attenuate pulmonary fibrosis through inhibiting TGF-β-WNT crosstalk [RNA-Seq]

city: San Francisco

first: Tsukasa

last: Kadota

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

summary: Idiopathic pulmonary fibrosis (IPF) is characterized by devastating and progressive lung parenchymal ﬁbrosis with poor prognosis. An aberrant recapitulation of lung developmental genes including transforming growth factor (TGF)-β and WNT has been widely implicated in the abnormal wound healing process following repetitive alveolar epithelial injury during IPF pathogenesis. Extracellular vesicles (EVs) including exosomes and microvesicles have been shown to carry various bioactive molecules and are involved in a variety of physiological and pathological processes. Here, we demonstrate that human bronchial epithelial cell-derived EVs (HBEC EVs) inhibited TGF-β-induced both myofibroblast differentiation and lung epithelial cellular senescence through attenuating WNT signaling. To ask how HBEC-EVs inhibited TGF-β-induced both myofibroblast differentiation and lung epithelial cellular senescence through attenuating WNT signaling, miRNA RNA-seq of HBEC-EVs was performed.

overall_design: EVs were isolated from the conditioned media of HBEC and BEAS2B (bronchial epithelial cell line) cells. Lung fibroblast were treated with HBEC EVs , BEAS2B EVs, or PBS(-) for 24hours or 48 hours. Total RNAs were extracted from these LFs and RNA-seq  analysis was performed.

first: Yu

last: Fujita

first: Jun

last: Araya

first: Yusuke

last: Yamamoto

first: Kazuyoshi

last: Kuwano

first: Takahiro

last: Ochiya


title: Human bronchial epithelial cell-derived extracellular vesicles attenuate pulmonary fibrosis through inhibiting TGF-β-WNT crosstalk

type: Non-coding RNA profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expansion of polyfuntional CD57+ KLRG1+ senescent CD4+ and CD8+ T cells in breast cancer patients.

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: We used microarrays to compare the gene expression profile of DP and DN (KLRG1 and CD57) CD4+ T cells from luminal breast cancer patients and healthy donors.

overall_design: [human mRNA] 9 samples: 3 KLRG1-CD57- (DN) T cells from breast cancer patients, 3 KLRG1+CD57+ (DP) T cells from breast cancer patients, 3 KLRG1+CD57+ (DP) T cells from healthy donors.

first: María

middle: C

last: Ramello

first: Carolina

middle: L

last: Montes

first: Eliane

last: Piaggio


title: Next Generation Sequencing of ileum in broiler infected with S. pullorum

city: Wuhan

first: fang

last: chen

state: Hubei

address: No1, Nanhu Road

country: China

institute: Hubei Academy of Agricultural Sciences

summary: This study was conducted to evaluate the effects of dietary supplemental magnolol and honokiol in broilers infected with S. pullorum. A total of 360 one-day-old broilers were selected and randomly divided into four groups with six replicates: the negative control group (CTL), S. pullorum-infected group (SP), and the S. pullorum-infected group supplemented with 300 mg/kg honokiol (SPH) or magnolol (SPM). Chicks in the SP, SPH, and SPM groups were orally treated with a 0.5 ml (4×108 CFU/mL) S. pullorum solution at 5 days of age, while chicks in the control (CTL)  group received the same amount of sterilized PBS at the same age.At 14 and 21 days of age, one chick from each replicate was randomly selected to be weighed and slaughtered by jugular exsanguination after a 12-h fasting period.  The ileum samples  were collected to analyze the differential expression genes.

overall_design: Examination of gene  in ileum microbiota of broiler infected with S. pullorum with or without magnolol and honokiol supplementation.

first: Fang

last: Chen


title: Gene signatures of sarcoma tumors with EWSR1-CREB fusion [RNA-seq]

city: New York

first: Fabio

last: Vanoli

state: NY

address: 1250 1st Avenue

institute: MSKCC

summary: We report RNA-seq for rare 3 rare entities of sarcoma tumors (AFH, CCS and GI-CCS) expressing the EWSR1-CREB1 and EWSR1-ATF1 oncogenic fusion

overall_design: RNA-seq of sarcoma tumors

first: Cristina

middle: R

last: Antonescu


title: The circulatory small non-coding RNA landscape in health and sepsis due to community-acquired pneumonia

city: Amsterdam

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC Locatie AMC

summary: We here sought to firstly identify differentially abundant circulatory small non-coding RNA in  critically ill patients with sepsis due to community-acquired pneumonia (CAP) patients as compared to healthy subjects, and secondly delineate those putatively targeted cellular pathways.

overall_design: RNA-Seq data of 13 critically ill patients with sepsis due to community-acquired pneumonia (CAP) and five healthy subjects.

middle: P


title: Human bronchial epithelial cell-derived extracellular vesicles attenuate pulmonary fibrosis through inhibiting TGF-β-WNT crosstalk [miRNA-Seq]

overall_design: EVs were isolated from the conditioned media of HBEC and BEAS2B (bronchial epithelial cell line) cells. Total RNAs were extracted from these EVs. miRNA-seq  analysis was performed using 20ng of EV miRNA.


title: FOXO activity adaptation safeguards the hematopoietic stem cell compartment in hyperglycemia

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Hematopoietic stem cells (HSC) activity is tightly controlled to ensure the integrity of the hematopoietic system during the organism’s lifetime. How the HSC compartment maintains its long-term fitness in condition of chronic stresses associated with systemic metabolic disorders is poorly understood. In this study, we show that obesity functionally affects the long-term function of the most immature engrafting HSC subpopulation. We link this altered regenerative activity to the oxidative stress and the aberrant constitutive activation of the AKT signaling pathway that characterized the obese environment. In contrast, we found minor disruptions of the HSC function in obese mice at steady state, suggesting that active mechanisms could protect the HSC compartment from its disturbed environment. Consistent with this idea, we found that FOXO proteins in HSCs isolated from obese mice become insensitive to their normal upstream regulators such as AKT, even during intense oxidative stress. We established that hyperglycemia, a key condition associated with obesity, is directly responsible for the alteration of the AKT-FOXO axis in HSCs and their abnormal oxidative stress response. As a consequence, we observed that HSCs isolated from a hyperglycemic environment display enhanced resistance to oxidative stress and DNA damage. Altogether, these results indicate that chronic metabolic stresses associated with obesity and/or hyperglycemia affect the wiring of the HSCs and modify their oxidative stress response. These data suggest that the uncoupling of FOXO to its environmental regulators could be a key adaptive strategy that promotes the survival of the HSC compartment in obesity.

overall_design: Cells were cultured in the presence or absence of BSO (100 µM). After culture, cells were washed with phosphate-buffered saline (PBS), and collected for RNA isolation.

first: Vinothini

last: Govindarajah

first: Jung-Mi

last: Lee

first: Michael

last: Solomon

first: Bryan

last: Goddard

first: Ramesh

last: Nayak

first: Kalpana

last: Nattamai

first: Hartmut

last: Geiger

first: Jose

last: Cancelas

first: Damien

last: Reynaud


title: Adoptive cell therapy using cultured tumor infiltrating lymphocytes for Japanese patients with refractory melanoma

city: Shinjuku-ku

first: Shigeki

last: Ohta

state: Tokyo

address: 6N1 35 Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University

summary:
Three patients who failed immune-checkpoint inhibitors were treated with the adoptive cell therapy using ex vivo cultured tumor infiltrating lymphocytes (TIL-ACT), which was composed of preparation of TIL culture, lympho-depleting non-myeloablative preconditioning, TIL infusion, and following relatively low dose intravenous IL-2 administration. Then we evaluated treatment feasibility, safety and clinical response.
To further investigate the relationship between the tumor microenvironment and the patient's clinical course,  we performed gene expression analysis of  the pre-treatment tumor cells and immunohistochemistry of the tumor tissue focusing on delineating the immune components and immunologic milieu within the tumor. Together with the results of genomic and immunological analysis of ex vivo cultured TILs by flowcytometry and quantitative real-time polymerase chain reaction, we considered the various immunostimulating or immunosupprrsive factors giving influence on the effects of the conducted TIL-ACT.

overall_design: Gene expression in melanoma cells sorted from metastatic tumor tissue was measured. Three independent experiments were performed using different donors for each experiment.


title: Lipopolysaccharide Alters the m6A Epitranscriptomic Tagging of RNAs in Cardiac Tissue

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

summary: N6-methyladenosine (m6A) modification plays important roles in the pathology of a variety of diseases. However, the roles of m6A modification in sepsis-induced myocardial dysfunction are not well defined.

overall_design: In this study, rats were divided into a control group and an lipopolysaccharide(LPS)-induced sepsis group. Global m6A levels of left ventricle tissue were measured by LC-MS/MS, and transcriptome-wide m6A modifications were profiled using epitranscriptomic microarrays (mRNAs and lncRNAs). Bioinformatics analysis was conducted to understand the functional implications of m6A modifications during sepsis. Methylated lncRNAs and mRNAs were measured by m6A single-base site qPCR.

first: Ye-Chen

last: Han

first: Hong-Zhi

last: Xie

first: Bo

last: Lu

first: Ruo-Lan

last: Xiang

first: Haipeng

last: Zhang

first: Jing-Yi

last: Li

first: Shu-Yang


title: Comprehensive and cell-type-based analysis of microRNA profiles and functions in mouse suprachiasmatic nucleus

city: Shanghai

first: Chuanzhen

last: Zhu

address: 320 Yueyang Road

institute: Institude of Neuroscience

summary: Circadian rhythm governs a variety of biological processes in essentially all living organisms and microRNAs have been found to play important roles in the post-transcriptional regulation of circadian clocks. However, the microRNA expression profile in mouse central circadian clock – suprachiasmatic nucleus (SCN) is lacking. In this study, we systematically profiled microRNAs in mouse SCN and SCN subtype neurons by high sensitive small RNA sequencing and examined their potential circadian functions. We found that a large fraction of known microRNAs are SCN-specific and 20 of them are also oscillated significantly. Predicted targets of these 20 microRNAs were enriched in circadian rhythm pathway as well. Integrated analysis of microRNA and mRNA revealed 3 clock-related functional modules, demonstrating the regulation roles of miR-24, miR-30, miR-7a, miR-7b, miR125a and miR125b in SCN. Furthermore, we observed distinct microRNA profiles in SCN subtype neurons with divergent regulatory functions, which correlated with their differential spatial distribution. In addition, we also identified a proportion of light-response microRNAs in SCN, one of which was miR-7a. Further experiments showed that miR-7a directly target fos and regulated its translation in SCN. All these observations indicate important circadian regulation roles of microRNA in central circadian clock.

overall_design: Examination of miRNA profiles in mouse SCN, hypothalamus and cortex; Examination of circadian miRNA profiles in mouse SCN; Examination of miRNA profiles in mouse SCN subtype neurons (AVP, VIP and CCK neurons); Examination of light-response miRNAs in mouse SCN

first: Jun

last: Yan


title: Pro- and anti-tumorigenic capacity of immunoproteasomes in shaping the tumor microenvironment

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Apart from the constitutive proteasome, the immunoproteasome that comprises the three proteolytic subunits LMP2, MECL-1 and LMP7 is expressed in most immune cells. In this study we describe two opposing roles for immunoproteasomes in regulating the tumor microenvironment. During chronic inflammation, immunoproteasomes modulated the expression of pro-tumorigenic cytokines and chemokines and enhanced infiltration of innate immune cells that led to the onset of colitis-associated carcinogenesies (CAC). In ulcerative colitis (UC) patients with high risk for CAC, immunoproteasome-induced pro-tumorigenic mediators were highly upregulated. Interestingly, the role for the same enzymatic complex in melanoma tumors is relatively unknown. We found that the high expression of immunoproteasomes in human melanoma was associated with better prognosis. Our data revealed that the immunoproteasome has a strong anti-tumorigenic function in cancer types with non-inflammatory microenvironment such as melanoma. CD8+ cytotoxic T lymphocytes (CTLs) from immunoproteasome-deficient mice were reduced during T cell homeostasis and were not able to combat melanoma efficiently. Our results indicate that the immunoproteasome exhibits either pro- or anti-tumoral properties in a context-dependent manner.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent Whole Human Genome (Agilent-012391) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Maik

last: Luu

first: Hanna

last: Leister

first: Ulrich

last: Steinhoff

first: Alexander

last: Visekruna


title: Developmental Circadian Disruption Alters Placental Signaling in Mice

city: Atlanta

first: Danielle

last: Clarkson-Townsend

state: Georgia

address: 1518 Clifton Road

department: Environmental Health

institute: Emory University

summary: We investigated the impacts of environmental circadian disruption on placental gene expression (E15.5) in a C57BL/6J mouse (Mus musculus) model. A number of transcripts showed sex-specific patterns of expression and several transcripts were differentially expressed in placenta from mice developmentally exposed to circadian disruption compared to mice exposed to control light.

overall_design: Female C57BL/6J mice were randomized into 2 different light treatments: standard control lighting (CL, 12:12 light:dark) schedule, or circadian disruption (inversions of the photoperiod every 3-4 days)). Females remained in this light treatment for 4 weeks of pre-dosing before timed breeding with male mice. Females remained in their light treatments until placental tissue collection at E15.5. Samples were collected from 6 pregnant mice in the CL group and 6 pregnant mice in the CD group. 2 placenta from each dam were selected for representation of a male and female sample (where possible) from each dam, for a total of 24 placenta samples. Isolated RNA were sequenced with PolyA RNA sequencing (paired-end) at a 30M read depth.

first: Machelle

last: Pardue


title: Dataset on transcriptome signature of skeletal muscle of young, adult and aged mice

city: Saint Genes Champanelle

first: Daniel

last: Bechet

address: Theix

department: UNH

institute: INRA

summary:
Skeletal muscle aging is characterized by a progressive decline in muscle mass and function, which is referred to as sarcopenia. However, the molecular mechanisms implicated in sarcopenia remain unclear.
In this dataset, we include the expression data obtained from gastrocnemius muscle of young, mature adult and old C57BL6 male mice.

overall_design: 18 Total samples were analyzed. Data were processed using GeneSpring GX 14.9 13 (Agilent) and analyzed by oneway ANOVA followed by pairwise comparisons using Tukey HSD post Hoc test. Benjamini-Hochberg multiple testing correction were performed to identify differentially expressed entities with a significance threshold set at P < 0.05. We generated the following pairwise comparisons using : 2 months vs. 11 months, 11 months vs. 25 months, 2 months vs. 25 months.

first: Anne

last: Listrat

first: Kheng

last: Goh


title: Tetrahexyldecyl Ascorbate (THDC) Degrades Rapidly under Oxidative Stress but Can Be Stabilized by Acetyl Zingerone to Enhance Collagen Production and Antioxidant Effects

status: Public on Aug 17 2021

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Tetrahexyldecyl Ascorbate (THDC) is an L-ascorbic acid precursor with improved stability and ability to penetrate the epidermis. The stability and transdermal penetration of THDC, however, may be compromised by the oxidant-rich environment of human skin. In this study, we show that THDC is a poor antioxidant that degrades rapidly when exposed to singlet oxygen. This degrada-tion, however, was prevented by combination with acetyl zingerone (AZ) as a stabilizing antiox-idant. As a standalone ingredient, THDC led to unexpected activation of type I interferon signaling, but this pro-inflammatory effect was blunted in the presence of AZ. Moreover, the combination of THDC and AZ increased expression of genes associated with phospholipid homeostasis and keratinocyte differentiation, along with repression of MMP1 and MMP7 expression, inhibition of MMP enzyme activity, and increased production of collagen proteins by dermal fibroblasts. Lastly, whereas THDC alone reduced viability of keratinocytes exposed to oxidative stress, this effect was completely abrogated by the addition of AZ to THDC. These results show that AZ is an effective antioxidant stabilizer of THDC and that combination of these products may improve ascorbic acid delivery. This provides a step towards reaching the full potential of ascorbate as an active ingredient in topical preparations.

overall_design: Gene expression profiling was performed using reconstituted human epidmeris (RHE, EpiDermFT™) tissues (MatTek, Ashland, MA; cat no. EFT-400, lot no. 29376). The experiment included 4 treatments with 5 replicates each (CTL = control, THDC = tetrahexyldecyl ascorbate, AZ = acetyl zingerone; THDC + AZ = tetrahexyldecyl ascorbate with acetyl zingerone in a 1:1 ratio). The samples were divided into two batched during the RNA extraction step (batch 1 and 2).

first: Manpreet

last: Randhawa

first: Geovani

last: Quijas

first: Krzysztof

last: Bojanowski

first: Ratan

last: Chaudhuri


title: Gene expression in the mouse embryo following early pregnancy exposure to ethanol or nicotine

city: Woolloongabba

first: Suyinn

last: Chong

state: QLD

address: 37 Kent St

country: Australia

institute: Mater Research Institute - The University of Queensland

summary: The in utero environment is a critical determinant of the immediate and future health of the developing fetus. Two of the most commonly used drugs during pregnancy are alcohol and nicotine. While prolonged gestational exposure to alcohol or nicotine has been associated with a range of adverse outcomes in the offspring, the consequences of exposure during early gestation only are less well understood. Here, we use mouse models of relatively moderate early gestational ethanol or nicotine exposure to profile gene expression in whole male embryos at 9.5 days post coitum using an Illumina microarray.

overall_design: Three treatment groups: ethanol-exposed (Ethanol), nicotine-exposed (Nicotine) and water (Control), with 12 replicates per group.

first: Lisa

last: Yamada


title: De novo Assembly of Royal Iris (Iris atropurpurea, section Oncocyclus) transcriptome

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Transcriptome sequencing of non-model organisms is valuable resource of the genetic basis of ecological-meaningful traits. The Royal Irises, Iris section Oncocyclus (Iris: Iridaceae, order Asparagales), are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises, which are a symbol of conservation in the Middle-east, serve as a model for evolutionary processes of speciation and plant ecology. However, there are not sufficient transcriptomic and genomic data for molecular characterization. Thus, it is necessary to generate massive transcript sequences for functional characterization and molecular marker development for the Royal Irises. The Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.

overall_design: In this work, we report the de novo assembly of a transcriptome for Iris atropurpurea, one of the Royal Irises species. This is the first reported transcriptome for this section, representing genes expressed in root, young leaf tissue and 3 flower development stages.

first: Yamit

last: Bar-Lev

first: Yuval

last: Sapir


title: Integrative Proteome, Transcriptome and DNA Methylome Analysis of Regulatory Networks During U937-derived Macrophage Polarization from an M2 to M1 Phenotype [array]

city: Nanning

first: Lequn

last: Li

state: Guangxi

address: Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, He Di Rd #71

institute: Guangxi Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Tumor associate macrophages (TAMs) depletion or re-education towards an antitumor effector phenotype are considered a promising cancer therapeutic approach. However, the underlying molecular mechanisms remain unclear. Here, we apply proteome, transcriptome  and DNA methylome to assay the regulatory networks during polarization of U937-derived macrophages transitioning from an M2 to M1 phenotype.

overall_design: We investigated the differential expression profiles of mRNA and lncRNA in U937 cells between two groups: the M2-U937 (M2 macrophages induced from M0 U937 cells), the M1 U937 (M1 macrophages produced from M2 macrophages). The data of each group are collected from independent experiments in triplicate. Transcriptomic analysis was carried out using a microarray (Arraystar Human lncRNA Gene Expression Microarrays V3.0; Agilent Technology, Santa Clara, USA), which includes about 30,586 LncRNAs and 26,109 coding transcripts.

first: Lqun

first: Honglin

last: Luo


title: BAZ2A-mediated repression via H3K14ac-marked enhancers promotes prostate cancer stem cells

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Prostate cancer (PCa) is one of the most prevalent cancers in men. PCa is clinically unpredictable; while most tumors are indolent, others exhibit lethal phenotypes. Current treatments of metastatic disease are not curative and lead to acquired resistance and relapse. Cancer stem cells (CSC) are thought to be associated with PCa relapse and represent a target against metastatic PCa. We isolated CSCs from metastatic PCa PC3 cells based on their ability to form spheres. We determined that TIP5, a factor previously implicated in aggressive PCa, is required for the formation of PCa spheres. We determined that TIP5-bromodomain (TIP5-BRD) is an epigenetic reader of H3K14ac. TIP5 genomic occupancy in PCa cells correlates with H3K14ac. We showed that a functional TIP5-BRD is required for the transition of PCa cells from a differentiated to a stem state. Mutations of TIP5-BRD or treatment with chemical probes that abrogate TIP5-BRD association with H3K14ac impair the formation of PCa spheres. Furthermore, treatment with TIP5-BRD inhibitors impairs the oncogenic transformation mediated by Pten-loss in PCa model organoids. Genome-wide occupancy analysis shows that TIP5 interacts with promoters of repressed genes in both PCa cells and metastatic tumors and with inactive enhancers that contain H3K14ac and are associated with genes implicated in developmental processes. Our findings indicate a role of TIP5 in PCa stem cell features and suggest potential epigenetic-reader therapeutic strategies to target TIP5 in aggressive PCa.

overall_design: Examination of 4 different histone marks between 2 cell types (PC3 cells and PCa spheres (tumorspheres with cancer stem cell features). Genomewide occupancy of BAZ2A and BAZ2A bromodomain mutant in PC3 cells. Transcriptomic analysis of BAZ2A depletion in PC3 cells.

first: R

last: Peña-Hernández

last: Aprigliano

first: S

last: Frommel

first: K

last: Pietrzak

last: Steiger

first: M

last: Roganowicz

first: L

last: Lerra

first: J

last: Bizzarro


title: High-throughout sequencing of triple negative breast cancer cells treated actived compound D16

city: wenzhou

first: Xiaohui

last: Zheng

address: Wenzhou Medical University, Chashan Street, Ouhai District, Wenzhou City, Zhejiang Province, China

department: College of Pharmacy

institute: Wenzhou Medical University

summary: The high-throughput sequencing technology was performed after the treatment of human triple negative breast cancer cells MDA-MB-231 with the active compound D16 designed and synthesized by ourselves, to explore the expression of genes related to cell proliferation, adhesion, migration and invasion of human triple negative breast cancer cells MDA-MB-231 after the treatment of the active compound Changes to explore the effect of active compounds on the proliferation and motility of triple breast breast cancer cells and to find an interesting target gene, CKAP2.

overall_design: Human triple negative breast cancer cells MDA-MB-231 were treated with active compound D16 at the concentration of 24µM for 48 hours.

first: Xiangxiang

last: Jin


title: Post-transcriptional control of mating-type gene expression during gametogenesis in Saccharomyces cerevisiae

city: NEW YORK

first: RUI

last: FU

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

summary: Short-read RNA-seq was performed on rRNA-depleted RNA isolated from spores of the budding yeast Saccharomyces cerevisiae that were sorted by mating type.

first: Randi

last: Yeager

first: Rui

last: Fu

first: Benjamin

last: Cooperman

first: Michael

last: McMurray


title: HOXB8 counteracts MAPK/ERK oncogenic signaling in a chicken embryo model of neoplasia

city: Marseille

first: Marie-Claire

last: DELFINI

address: Campus de Luminy

institute: IBDM / CNRS

summary: HOX transcription factors are members of an evolutionarily conserved family of proteins required for the establishment of the anteroposterior body axis during bilaterian development.  Although they are often deregulated in cancers, the molecular mechanisms by which they act as oncogenes or tumor suppressor genes are only partially understood. Since the MAPK/ERK signaling pathway is deregulated in most cancers, we aimed at apprehending if and how Hox proteins interact with ERK oncogenicity.   Using an in vivo neoplasia model in the chicken embryo that we have developed, consisting in the overactivation of the ERK1/2 kinases in the trunk neural tube, we analyzed the consequences of HOXB8 gain of function at morphological and transcriptional level in this model. We found that HOXB8 acts as a tumor suppressor, counteracting ERK-induced neoplasia. HOXB8 tumor suppressor function in this model relies on a large reversion of the oncogenic transcriptome induced by ERK. In addition to showing that HOXB8 protein controls the transcriptional responsiveness to ERK oncogenic signaling, our study identified new downstream targets of ERK oncogenic activation in an in vivo context that could provide clues for therapeutic strategies.

overall_design: Neural tube in ovo electroporations were performed at HH11. Two pCIG controls, two pCIG-MEK1ca, two pCIG-HoxB8 and two pCIG-MEK1ca+pCIG-HoxB8 experiments were performed. GFP-expressing cells were FACS-isolated and total polyA RNA sequenced.

first: Axelle

last: Wilmerding

first: Lauranne

last: Bouteille

first: Lucrezia

last: Rinaldi

first: Nathalie

last: Caruso

first: Yacine

last: Graba

last: Delfini


title: A chromatin immunoprecipitation database for prokarytic organisms [E. coli K-12 MG1655 ArcA]

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in E. coli K-12 MG1655. Here, we present the genome-wide binding for major TFs in the E. coli K-12 MG1655.

overall_design: Identification of genome-wide bindings for transcription factors in E. coli K-12 MG1655, using ChIP-exo technology

first: Bernhard

last: Palsson


title: A chromatin immunoprecipitation database for prokarytic organisms [E. coli K-12 MG1655 mixTF]


title: A chromatin immunoprecipitation database for prokarytic organisms

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Refer to individual Series


title: Elucidation of the CodY target genes in Staphylococcus aureus USA300 using ChIPexo

summary: CodY is a highly conserved global transcriptional factor that regulates the expression of dozens of genes related to metabolism and virulence in Staphylococcus aureus. The S. aureus CodY regulon has been studied in vitro. However, in vivo CodY DNA-binding activity and the identity of the corresponding target genes remain unknown due to lack of a ChIP-grade monoclonal antibody. Using a novel CodY monoclonal antibody that we developed in established ChIP-exo protocols, we report in vivo target genes of CodY in two S. aureus USA300 clinical strains (TCH1516 and LAC). The total number of CodY-binding sites exceeded 110, but their location varied between the two strains. The majority of the identified binding sites were located within the promoter regions. Based on the sequences of the CodY-binding sites, a model of CodY interaction with DNA is proposed. Furthermore, S. aureus CodY protein is highly conserved across a G+C Gram-positive species, including Bacillus subtilis and Listeria monocytogenes, and thus this study paves the way for exploration of the differential binding of CodY among a range of gram-positive species, including pathogenic ones

overall_design: Identification of genome-wide bindings for Staphylococcus aureus CodY, using ChIP-exo technology


title: Response of SCLC to mutant KRAS or EGFR induction

city: Vancouver

first: William

last: Lockwood

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: BC Cancer

summary: Lineage transformation between lung cancer subtypes is a poorly understood phenomenon associated with resistance to treatment and poor patient outcomes. Here, we aimed to model this transition in order to define underlying biological mechanisms and identify potential avenues for therapeutic intervention. Small cell lung cancer (SCLC) is neuroendocrine in origin and, in contrast to non-SCLC (NSCLC), rarely contains mutations that drive the MAPK pathway. Likewise, NSCLCs that transform to SCLC concomitantly with development of therapy resistance downregulate MAPK signaling, suggesting an inverse relationship between pathway activation and lineage state. To test this, we activated MAPK in SCLC through conditional expression of mutant KRAS or EGFR, which revealed suppression of the neuroendocrine differentiation program via ERK. We found that ERK induces the expression of ETS factors, phenocopying ERK-mediated effects on transformation into the NSCLC-like phenotype. ATAC-seq demonstrated ERK-driven changes in chromatin accessibility at putative regulatory regions and global chromatin rewiring at neuroendocrine and ETS transcriptional targets. Further, induction of ETS factors as well as suppression of neuroendocrine differentiation were dependent on histone acetyltransferase activities of CBP/p300. Overall, we describe how the ERK-CBP/p300-ETS axis promotes a lineage shift between neuroendocrine and non-neuroendocrine lung cancer phenotypes and provide rationale for the disruption of this program during transformation-driven resistance to targeted therapy.

overall_design: Two SCLC cell lines (H82 and H2107) were transduced with doxycyline inducible lentivirial vectors containing either GFP, mutant EGFR (L858R) ot mutant KRAS (G12V). Cell were placed on doxcycline to induce gene expression, and RNA harvested at the points indicated for expression analysis using Affymetrix arrays. In total, three biological replcates were analyzed for each gene at three timepoints after addition of Dox: Day 0 (No Dox), Day 1, and Day 7 for a total of 54 samples. GFP at each time point serves as a reference.

middle: W

first: Yusuke

last: Inoue


title: Assessing the toxicity of 17α-ethinylestradiol in rainbow trout using a four-day transcriptomics benchmark dose (BMD) embryo assay

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

institute: University of Saskatchewan

summary: There is an urgent demand for more efficient and ethical approaches in chemical risk assessment.  Using 17α-ethinylestradiol (EE2) as a model compound, this study established a live-animal alternative  embryo benchmark-dose (BMD) assay for rainbow trout (RBT; Oncorhynchus mykiss) to derive transcriptomic points-of-departure (tPODs).  Embryos were exposed to graded concentrations of EE2 (0, 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L) from hatch to 4 and up to 60 days post-hatch (dph) to assess molecular and apical responses, respectively.  Whole proteome analyses of alevins did not show clear estrogenic effects, while transcriptomics revealed responses that were in agreement with apical effects including excessive accumulation of intravascular and hepatic proteinaceous fluid and significant increases in mortality at 55.1 and 169 ng/L EE2 at later time points.  Transcriptomic BMD analysis estimated the median of the 20th lowest geneBMD to be  0.18 ng/L; the most sensitive tPOD.  Other estimates (0.78, 3.64, and 1.63 ng/L for the tenth percentile geneBMD, first peak geneBMD distribution, and median geneBMD of the most sensitive overrepresented pathway, respectively) were within the same order of magnitude as empirically derived apical P ODs for EE2 in the literature.  This 4-day alternative RBT embryonic assay was effective in deriving protective tPODs for EE2.

overall_design: mRNA profiles of whole rainbow trout alevins (Oncorhynchus mykiss; 4 days post hatch) exposed to solvent control (0.01% DMSO), 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L 17a-ethinylestradiol (measured concentrations)  from hatch to 4 days post-hatch. Three replicates of pooled alevins (3 alevins per replicate) per treatment group.

first: Alper James

last: Alcaraz

first: Kamil

last: Mikulášek

first: David

last: Potěšil

first: Bradley

last: Park

first: Kamran

last: Shekh

first: Burbridge

last: Connor

first: Zbyněk

last: Zdráhal

last: Schneider

first: Doug

last: Crump

first: Niladri

last: Basu


title: ATAC-seq of lung cancer cell lines with doxycycline KRAS G12V and drug treatments

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: We modelled the effects of KRAS activation on three SCLC cell lines H2107, H82, H524 and investigated the effects of KRAS induction and various drug treatments on motif and chromatin accessibility profiles.

overall_design: H2107-KRAS G12V and H524-KRAS G12V cells treated with doxycycline ± SCH772984 (1 μM) for 72 hours. H82-KRASG12V cells were treated with the following chemicals: doxycycline; doxycycline + SCH772984 (1 μM); doxycycline + SB747651A (5 μM); doxycycline + A-485 (400 nM); or doxycycline + SB747651A (5 μM) + A-485 (400 nM). After 72 hours treatment, these cells as well as corresponding non-treated control cells were collected and frozen.

first: Ana

last: Nikolic

first: Alvin

last: Liu

first: Marc

last: Ladanyi

first: Romel

last: Somwar


title: mRNAseq of murine PancOVA tumor cells after coculture with murine qPSCs, myCAFs or iCAFs

city: Marburg

first: Magdalena

last: Huber

institute: Philipps-University Marburg

summary: To assess the influence of various fibroblast populations on the tumor cells in the PDAC microenvironment in Vitro,a co-culture of murine PancOVA tumor cells and quiescent (qPSC) or activated and primed inflammatory  (iCAF) or myofibroblastic (myCAF) Fibroblasts was established, FACS sorted into fibroblast and tumor cell fractions after 48h and mRNA sequencing of PancOVA tumor cells from this coculture was performed

overall_design: Fibroblasts and PancOVA cells were seeded as co-cultures for 48h in matrigel droplets. All conditions (iCAF, myCAF, qPSC) were done in triplicates, non-activated (qPSC) fibroblasts were used as background expression control.

first: Felix

last: Picard

first: Veronika

last: Lutz

first: Anna

last: Brichkina

last: Hupfer

first: Hartmann

last: Raifer

first: Matthias

last: Klein

first: Ho-Ryun

last: Chung


title: Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

institute: Utrecht University


title: Spatial Transcriptomics Analysis of Uterine Gene Expression in Enhancer of Zeste Homolog 2 (Ezh2) Conditional Knockout Mice

city: Columbia

first: Cheryl

last: Rosenfeld

state: MO

address: 1201 Rollins Street

department: BIOMEDICAL SCIENCES

institute: University of Missouri.edu

summary: Histone proteins undergo various modifications that alter chromatin structure, including addition of methyl groups. Enhancer of homolog 2 (EZH2), is a histone methyltransferase that methylates lysine residue 27, and thereby, suppresses gene expression. EZH2 plays integral role in the uterus and other reproductive organs. We have previously shown that conditional deletion of uterine EZH2 results in increased proliferation of luminal and glandular epithelial cells, and RNAseq analyses reveal several uterine transcriptomic changes in Ezh2 conditional (c) knockout (KO) mice that can affect estrogen signaling pathways. To pinpoint the origin of such gene expression changes, we used the recently developed spatial transcriptomics (ST) method with the hypotheses that Ezh2cKO mice would predominantly demonstrate changes in epithelial cells and/or ablation of this gene would disrupt normal epithelial/stromal gene expression patterns. Uteri were collected from ovariectomized adult WT and Ezh2cKO mice and analyzed by ST. Asb4, Cxcl14, Dio2, and Igfbp5 were increased, Sult1d1, Mt3, and Lcn2 were reduced in Ezh2cKO uterine epithelium vs. WT epithelium. For Ezh2cKO uterine stroma, differentially expressed key hub genes included Cald1, Fbln1, Myh11, Acta2, and Tagln. Conditional loss of uterine Ezh2 also appears to shift the balance of gene expression profiles in epithelial vs. stromal tissue toward uterine epithelial cell and gland development and proliferation, consistent with uterine gland hyperplasia in these mice. Current findings provide further insight into how EZH2 may selectively affect uterine epithelial and stromal compartments. Additionally, these transcriptome data might provide the mechanistic understanding and valuable biomarkers for human endometrial disorders with epigenetic underpinnings.

overall_design: Eight uteri were collected from ovariectomized adult WT and Ezh2cKO mice

last: Mesa

first: Jiude

last: Mao

first: Theresa

middle: I

last: Medrano

first: Nathan

middle: J

last: Bivens

first: Alexander

last: Jurkevich

first: Geetu

last: Tuteja

first: Paul

last: Cooke


title: An NF-κB/IRF1 axis programs cDC1 to drive antitumor immunity II

status: Public on Aug 16 2021

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: functions of cDC1s are poorly understood. We mapped the molecular pathways regulating intratumoral cDC1 maturation using single cell RNA sequencing. We identified NF-κB and IFN pathways as being highly enriched in a subset of functionally mature cDC1s. The specific targeting of NF-κB or IFN pathways in cDC1s prevented the recruitment and activation of CD8+ T cells and the control of tumor growth. We identified an NF-κB-dependent IFN-γ-regulated gene network in cDC1s, including cytokines and chemokines specialized in the recruitment and activation of cytotoxic T cells. We used single cell transcriptomes to map the trajectory of intra-tumoral cDC1 maturation which revealed the dynamic reprogramming of tumor-infiltrating cDC1s by NF-κB and IFN signaling pathways. This maturation process was perturbed by specific inactivation of either NF-κB or IRF1 in cDC1s, resulting in impaired expression of IFN-γ-responsive genes and consequently a failure to efficiently recruit and activate anti-tumoral CD8+ T cells. Finally, we demonstrate the relevance of these findings to cancer patients, showing that activation of the NF-κB/IRF1 axis in association with cDC1s is linked with improved clinical outcome. The NF-κB/IRF1 axis in cDC1s may therefore represent an important focal point for the development new diagnostic and therapeutic approaches to improve cancer immunotherapy.

overall_design: We performed bulk RNA-seq analysis of cDC1s sorted from YUMM1.7 tumors in female IkbkbF/F and IkbkbΔXcr1 mice.

first: G

last: Ghislat

first: TP

first: M

last: Dalod

first: T

last: Lawrence


title: Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat

city: Vienna

first: Alwin

last: Köhler

state: Vienna

address: Dr. Bohr-Gasse 9/3

department: Medical Biochemistry

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

summary: Transcriptome analysis of ino4∆ and Mga2∆TM-overexpressing cells in order to understand the mechanism by which cells decide whether to synthesize LDs from the INM or not. A striking difference between the transcriptomes of Mga2∆TM-overexpressing cells (cLDs) and ino4∆ cells (cLDs and nLDs) is the fact that enzymes involved in PL synthesis, for example, the phosphatidylethanolamine methyltransferase CHO2 or the phospholipid methyltransferase OPI3, are downregulated specifically in ino4∆ cells. In contrast, Mga2∆TM overexpressing cells showed an upregulation of the Ole1 desaturase and Mvd1, an enzyme involved in sterol biosynthesis, whereas the expression of PL synthesis factors remained largely unchanged.

overall_design: RNA-Seq of 7 different yeast strains to investigate which genes are responsible for nLD production; 3 replicates for each.

first: Anete

last: Romanauska


title: RiboTag-IP-RNA sequencing of parvalbumin neurons in frontal cortex of Fxr1 knockout mice

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

summary: We report the genome-wide gene expression in parvalbumin neurons in frontal cortex of of Fxr1 knockout mice

overall_design: Examination of translatome of parvalbumin neurons in frontal cortex of Fxr1 knockout mice

first: Yu

last: Gao

first: Minjie

last: Shen


title: Serum microRNAs as xerostomia biomarkers in oropharyngeal cancer patients undergoing radiotherapy

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary: Severe xerostomia is noted in the majority of patients irradiated for oropharyngeal cancer (OPC). Extracellular microRNAs (miRNAs) may serve as effective tools allowing prediction of radiation-related toxicity. The aim of this study was to create an efficient prognostic miRNA-based test for severe, patient-rated xerostomia 3 months after primary treatment. This prospective study enrolled OPC patients treated between 2016 and 2018 in three centers in Poland. The primary endpoint was severe (grade ≥3) xerostomia as assessed by the EORTC H&N-35 questionnaires. Initially, a group of 10 patients with severe xerostomia was randomly selected and matched with a comparative group of 10 patients without severe xerostomia. Samples were collected before RT, after receiving 20 Gy and within 24 hours after treatment completion. qPCR arrays (QIAGEN, Hilden, Germany) were used to quantify expression levels of 752 miRNAs in the serum at all timepoints. The resulting logistic-regression based model was validated in additional 60 patients: 30 with grade >3 xerostomia and 30 without. Of 152 eligible patients, we successfully recruited 111 patients. Severe xerostomia 3 months after treatment was reported by 63 patients (56.8%). Mean dose delivered to parotid glands was higher in both exploratory and validation cohort. The model based on miR-185-5p and miR-425-5p expression levels measured before the start of radiotherapy had AUC 0.96 (95% CI: 0.88-1.00). The model based on the same miRNAs remained robust when parameters were measured after 20 Gy (AUC 0.90 (95% CI: 0.75-1.00)). These results were confirmed in the validation group. In the validation group pre-radiotherapy model application yielded 73.3% sensitivity and 80.0% specificity. In the samples taken after 20 Gy, the same two miRNAs yielded 67.7% sensitivity and 72.4% specificity. The model including pretreatment miR-185-5p and miR-425-5p levels together with mean parotid dose, yielded 90.0% sensitivity and 80.0% specificity. In the validation cohort, this model yielded 80.6 % sensitivity and 55.2 % specificity. The model based on miRNA levels measured after 20 Gy and mean parotid dose had 80.0 % sensitivity and 100% specificity in the exploratory group. In the validation cohort its performance fell to 71.0 % sensitivity and 58.6 % specificity. Serum expression levels of miR-425-5p and miR-185-5p measured before the start of radiotherapy or during therapy (after 20 Gy) had a significant prognostic value for the occurrence of severe xerostomia 3 months after treatment completion. The variability explained by miRNAs appears to be, at least partially, independent from the one related to the dosimetric data.

overall_design: Serum samples were collected prior to radiotherapy, after receiving 20 Gy, within 24 hours after treatment completion and stored in -80°C. Total RNA was isolated from 200 μL serum samples using miRCURY RNA Isolation kit (QIAGEN, Hilden, Germany). cDNA synthesis was performed using miRCURY LNA RT Kit (QIAGEN, Hilden, Germany). We used real-time PCR arrays with locked nucleic acid-containing primers (miRCURY LNA miRNA miRNome PCR Panels; QIAGEN, Hilden, Germany) for serum profiling of 138 miRNAs.

first: Bartłomiej

last: Tomasik


title: Chromatin integration labeling for mapping multiple DNA binding proteins and modifications with low input.

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We established a novel epigenomic profiling method multi–target ChIL–seq, mtChIL-seq, which enables the detection of the DNA binding proteins and histone modifications simultaneously using a same sample.

overall_design: We performed mtChIL-seq on C2C12 cells with various cell numbers (100, 1k and 10k cells) against various histone modifications and DNA binding proteins.

first: Hiroshi

last: Kimura

first: Kazumitsu

last: Maehara

first: Akihito

last: Harada

first: Tetsuya

last: Handa


title: RNA-seq analysis of CAR-NKAE cells and CD45RA- CAR-T cells

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: CAR-T cell therapy against MM currently shows promising results, but usually with serious toxicities. CAR-NK cells may exert less toxicity when redirected against resistant myeloma cells. CARs can be designed through the use of receptors, such as NKG2D, which recognizes a wide range of ligands to provide broad target specificity. Here, we test this approach by analyzing the anti-tumor activity of activated and expanded NK cells (NKAE) and CD45RA- T cells from MM patients that were engineered to express an NKG2D-based CAR. NKAE cells were cultured with irradiated Clone9.mbIL21 cells. Then, cells were transduced with an NKG2D-4-1BB-CD3z-CAR. CAR-NKAE cells exhibited no evidence of genetic abnormalities. Although memory T cells were more stably transduced, CAR-NKAE cells exhibited greater in vitro cytotoxicity against MM cells, while showing minimal activity against healthy cells. In vivo, CAR-NKAE cells mediated highly efficient abrogation of MM growth, and two of the treated mice remained disease-free. Overall, these results demonstrate that it is feasible to modify autologous NKAE cells from MM patients to safely express a NKG2D-CAR. Additionally, autologous CAR-NKAE cells display enhanced anti-myeloma activity demonstrating that they could be an effective strategy against MM supporting the development of NKG2D-CAR NK cell therapy for MM.

overall_design: Five paired samples of activated and expanded natural killer cells (NKAE) and NKG2-CAR-transduced NKAE cells and two paired samples of CD45RA- T cells and CD45RA- NKG2D CAR-T cells were analyzed

first: Alejandra

last: Leivas

first: Laura

last: Sánchez

last: Graña-Castro

first: Joaquín

last: Martínez


title: No adverse effect of a parental low protein/high carbohydrate diet on their offspring, in rainbow trout (liver)

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

institute: INRA

summary: In rainbow trout (Oncorhynchus mykiss), the effect of a paternal and a maternal "high carbohydrate/low protein" diet was assessed on progeny. To this purpose, two-year old males and females rainbow trout were fed either a control diet or a "high carbohydrate/low protein" diet for an entire reproductive cycle for females and for 5  months for males. Crossed-fertilizations were carried out in order to obtain 4 groups of offspring. Offspring were fed with a commercial diet until they reached a market size. At this stage, hepatic transcriptomes were compared to detect any impact of the parental diet on offspring metabolism.

overall_design: Two-year old male and female rainbow trout were fed either a control diet (NC, 63.89% protein and 0% carbohydrates) or a "high carbohydrate/low protein" diet (HC/LP, 42.96% protein and 35.30% carbohydrates) for an entire reproductive cycle for females and for 5 months for males. During the spawning period, spawns from NC and HC/LP females were cross-fertilized with milts from males from each experimental condition. Thus, offspring from 4 different conditions were obtained: NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the HC/LP diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet). Offspring were reared into 9 tanks (n=3/condition) in a  flow-though rearing system supplied with natural spring water at 17°C. Since their first feeding,  fish were fed ad libitum with a commercial diet (T3-P Omega, Skretting, France). After 36 weeks of feeding, liver were sampled in offspring (n=6 per confition).

first: T

first: S

last: Panserat

first: L

last: Marandel


title: GIV/Girdin Regulates Spatiotemporal Signaling during Sperm Capacitation and is Required for Male Fertility

city: LA JOLLA

first: Sahar

last: Taheri

state: California

address: 9500 GILMAN DR.

summary: For a sperm to successfully fertilize an egg, it must first undergo capacitation in the female reproductive tract, and later undergo acrosomal reaction (AR) upon encountering an egg. How premature AR is avoided despite rapid surges in signaling cascades during capacitation remains unknown. Using a combination of KO mice and cell-penetrating peptides, here we show that GIV (CCDC88A), a guanine nucleotide-exchange factor (GEM) for trimeric GTPases, is highly expressed in spermatocytes and is required for male fertility. GIV is rapidly phosphoregulated on key tyrosine and serine residues in human and murine sperms. These phosphomodifications enable GIV-GEM to orchestrate two distinct compartmentalized signaling programs in the sperm tail and head; in the tail, GIV enhances PI3K→Akt signals, sperm motility and survival, whereas in the head it inhibits cAMP surge and premature AR. Furthermore, GIV transcripts are downregulated in the testes and semen of infertile men. These findings exemplify the spatiotemporally segregated signaling programs that support sperm capacitation and the etiology of infertility in men.

overall_design: Eight-week-old conditional GIV-KO mice (Girdin fl/fl-UBC-Cre-ERT2; n = 4) or WT littermate controls (Girdin fl/fl; n = 3) were injected with Tamoxifen (i.p, 5 consecutive days), followed by co-housing with females for assessing the total number of live births over time and litter sizes. Testes were harvested at the end of study and analyzed by RNA Seq.

first: Debashis

last: Sahoo

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Cooperativity between classical DNA end-joining and p53 in carboplatin resistance in human ovarian cancer cells

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

institute: CHA University

summary: Targeting classical end-joining signaling pathway might be a potential therapeutic strategy to overcome the chemotherapeutic drug resistance and increase the potency of cancer treatment

overall_design: To investigate the key regulator of carboplatin-resistance in human ovarian cancer cells, DNA repair status of 3 different human ovarian cancer cells with different degree of carboplatin-resistance was compared.

first: Youn-Jung

last: Kang

first: Min-Ji

last: Yoon

first: Jungho

last: Ahn

first: Hwijae

last: Cha

first: Danbi

last: Lee

first: Hyun-Seok

last: Jeong


title: No adverse effect of a parental low protein/high carbohydrate diet on their offspring, in rainbow trout (muscle)

summary: In rainbow trout (Oncorhynchus mykiss), the effect of a paternal and a maternal high carbohydrate-low protein diet was assessed on progeny at long term. To this purpose, two-year old male and female rainbow trout were fed either a control diet or a high carbohydrate/low protein diet for an entire reproductive cycle for females and for 5  months for males. Crossed-fertilizations were carried out in order to obtain 4 groups of offspring. Offspring were fed with a commercial diet until they reached a market size. At this stage, muscle transcriptomes were analysed to detect any effect of the parental diet on offspring metabolism.

overall_design: Two-year old male and female rainbow trout were fed either a control diet (NC, 63.89% protein and 0% carbohydrates) or a "high carbohydrate/low protein" diet (HC/LP, 42.96% protein and 35.30% carbohydrates) for an entire reproductive cycle for females and for 5 months for males. During the spawning period, spawns from NC and HC/LP females were cross-fertilized with milts from males from each experimental condition. Thus, offspring from 4 different conditions were obtained: NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the HC/LP diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet). Offspring were reared into 9 tanks (n=3/condition) in a  flow-though rearing system supplied with natural spring water at 17°C. Since their first feeding,  fish were fed ad libitum with a commercial diet (T3-P Omega, Skretting, France). After 36 weeks of feeding, muscle were sampled in offspring (n=6 per confition).


title: No adverse effect of a parental low protein/high carbohydrate diet on their offspring, in rainbow trout

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: An NF-κB/IRF1 axis programs cDC1 to drive antitumor immunity

first: Thien-Phong

last: Vu Manh

summary: Conventional type 1 dendritic cells (cDC1s) are critical for anti-tumor immunity. They acquire antigens from dying tumor cells and cross-present them to CD8+ T cells, promoting the expansion of tumor-specific cytotoxic T cells. However, the signaling pathways that govern the anti -tumor functions of cDC1s are poorly understood. We mapped the molecular pathways regulating intratumoral cDC1 maturation using single cell RNA sequencing. We identified NF κB and IFN pathways as being highly enriched in a subset of functionally mature cDC1s. The specific targeting of NF-κB or IFN pathways in cDC1s prevented the recruitment and activation of CD8+ T cells and the control of tumor growth. We identified an NF-κB-dependent IFN-γ-regulated gene network in cDC1s, including cytokines and chemokines specialized in the recruitment and activation of cytotoxic T cells. We used single cell transcriptomes to map the trajectory of intra-tumoral cDC1 maturation which revealed the dynamic reprogramming of tumor-infiltrating cDC1s by NF-κB and IFN signaling pathways. This maturation process was perturbed by specific inactivation of either NF-κB or IRF1 in cDC1s, resulting in impaired expression of IFN-γ-responsive genes and consequently a failure to efficiently recruit and activate anti-tumoral CD8+ T cells. Finally, we demonstrate the relevance of these findings to cancer patients, showing that activation of the NF-κB/IRF1 axis in association with cDC1s is linked with improved clinical outcome. The NF-κB/IRF1 axis in cDC1s may therefore represent an important focal point for the development new diagnostic and therapeutic approaches to improve cancer immunotherapy.

overall_design: 14 samples were analysed, each sample is a tumor grown in an individual mouse, no replicates were included. Controls are Ikbkb_FF and Irf1_FF. Reference samples are Ikbkb_dXCR1 and Irf1_dXCR1.

first: G

last: Ghislat

first: A

last: Cheema

first: N

last: Attaf

first: C

last: Dong

first: P

last: Milpied

first: M

last: Dalod

last: Lawrence


title: mRNA expression profiling A549 lung cancer cells following PPARGC1A suppression

city: Chungju-si

first: Ji Hong

last: Lim

address: 268, Chungwon-daero

institute: Konkuk University

summary: PPARGC1A oppositely regulates cancer metastasis in melanoma, breast, and pancreatic cancer; however, little is known about its impact on lung cancer metastasis. We generated gene-expression profile of control and PPARGC1A suppressed A549 cells, a lung adenocarcinoma cell line that expresses moderate levels of PPARGC1A to investigate the role of this gene in lung cancer metastasis.

overall_design: Lentivirus expressing shRNA against PPARGC1A or control was infected into A549 lung cancer cells.  The infected cells were selected with puromycin for 5 days, and then total RNA was used to analyze gene expression profiling.

first: Min-Gyu

first: Hyun-Woo

last: Shin

first: Ji-Hong


title: Evading immune evasion via reprograming of the tumor microenvironment by radiotherapy and simultaneous targeting of TGF-β/PD-L1

city: Arlington

first: George

last: Locke

state: Massachusetts

department: Translational Medicine

institute: EMD Serono

summary: Tumor immunogenicity enhanced by radiotherapy (RT), is often counterbalanced by immune evasive mechanisms and tissue remodeling effects via upregulation of transforming growth factor-β (TGF-β) and programmed cell death-ligand 1 (PD-L1). We report that bintrafusp alfa (BA), a bifunctional fusion protein that simultaneously inhibits TGF-β and PD-L1, is a favorable combination partner for RT in eradicating multiple treatment-resistant tumor models. Beneficial effects of BA+RT (BART) are partly attributed to counterbalancing undesired RT effects and local tumor microenvironment reprograming, leading to reconstitution of tumor immunity and regression of spontaneous lung metastases. Intriguingly, BA, but neither TGF-β trap nor anti–PD-L1 alone, attenuates late-stage RT-induced lung fibrosis. Single cell transcriptome show TGF-β expression is confined to PD-L1+ endothelium and M2/lipofibroblast-like cells. Hence, superior effects of BA could be attributed to its ability to trap TGF-β to relevant PD-L1+ compartments. Here, we provide rationales that BART resensitizes tumors and broadens the therapeutic window.

overall_design: 4T1 cells, 0.5 × 105, were inoculated im in the thigh of BALB/c mice on day -6, mice were treated on day 0  (n = 9 mice/group) and euthanized on day 6. To assess the combination of radiation with Bintrafusp alfa (BA), mice were randomized into the following treatment groups: isotype control (400 μg), RT (exact dose and schedule provided in the figure legends) + isotype control, BA (492 μg), or BA + RT (BART). For transcriptome analysis of 4T1 tumors, total RNA was extracted and RNA sequencing (RNAseq) analyses were performed using a targeted mouse Immuno-Oncology panel (RMM-009Z, Qiagen) and a Qiaseq targeted RNA custom panel (Qiagen) with RT2 Profiler PCR arrays containing murine genes related to TGF-β signaling targets (PAMM-235Z), DNA damage signaling pathway (PAMM-029Z), DNA repair (PAMM-042Z), and fibrosis (PAMM-120Z).

first: Yan

last: Lan

first: Mahmoud

last: Moustafa

first: Maximillian

last: Knoll

first: Adam

last: Lazorchak

first: Jennifer

last: Furkel

first: Chunxiao

last: Xu

first: Tsz-Lun

last: Yeung

first: Mohammad

last: Hasheminasab

first: Molly

last: Jenkins

first: Sarah

last: Meister

first: Huakui

last: Yu

first: Julian

last: Schlegel

first: Bo

last: Marelli

first: Zili

last: Tang

first: Guozhong

last: Qin

first: Carmen

last: Klein

first: Jin

last: Qi

first: Cheng

last: Zhou

first: Damir

last: Krunic

first: Melissa

last: Derner

first: Christian

last: Schwager

first: Rachel

middle: E

last: Fontana

first: Katrin

last: Rein

first: Mark

last: Kriegsmann

first: Juergen

last: Debus

first: Katharina

first: Kin-Ming

last: Lo

first: Amir

last: Abdollahi


title: A chromatin immunoprecipitation database for prokarytic organisms [Staphylococcus aureus]

status: Public on Aug 15 2021

city: La Jolla

first: Ye

last: Gao

institute: UCSD

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Here, we present the genome-wide binding for major TFs in Staphylococcus aureus USA300 strains.

overall_design: Identification of genome-wide bindings for transcription factors in Staphylococcus aureus using ChIP-exo technology

first: Bernhard

last: Palsson


title: Induction of trophoblast stem cells from human pluripotent stem cells [ChIP-seq]

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

summary: In human, the functional placenta requires the proper differentiation of trophoblastic subtypes from the trophoblast stem cells (hTSCs). Although successful derivation of hTSCs from the early placentas and blastocysts, these hTSCs face ethical concerns and limited models for trophoblast-related disorders at later stage, such as preeclampsia. Here, we show that both hESCs and hiPSCs are able to be induced to the long-term and proliferative hTSCs under defined culture medium. These induced trophoblast stem cells (iTSCs) are comparable to the hTSC cell line derived from blastocyst in morphology, growth properties, specific genes expression, capacity of differentiating toward extravillous cytotrophoblast and syncytiotrophoblast, and patterns of transcriptome profile, chromatin accessibility and histone modification that are conducive to placenta development and maintenance of hTSCs. Notably, iTSCs meet four criteria defining "trophoblastic" including: expression of specific transcript factors, hypomethylation of ELF5 promoter, lack of expression of HLA-class I molecules and expression of the chromosome 19-encoded miRNA. Moreover, we reveal that addition of BMP4 or absence of H3K27 methyltransferases EZH1/2 could enhance the iTSCs generation. Our results suggest that human TS cells could be derived from human pluripotent stem cells, which expands the source of human TS cells avoiding ethic issues and provides a useful tool for researching placenta development and function, and modeling placenta-originated disorders.

overall_design: We compared the H3K27me3  and H3K4me3 binding sites of human trophoblast stem cells and human embryonic stem cells by ChIP-seq.

first: Yongli

last: Shan


title: Induction of trophoblast stem cells from human pluripotent stem cells [ATAC-seq]

overall_design:
We compared the chromatin accessibility of  human trophoblast stem cells and human embryonic stem cells by ATAC-seq.

Please note that each processed data was generated from both replicates and is linked to the corresponding first replicate records.

first: Yanxing

last: Wei


title: Induction of trophoblast stem cells from human pluripotent stem cells


title: mRNA-seq analysis of the Tat mutant of extra-intestinal pathogenic E. coli

city: Wuhan

first: Qi

last: Huang

state: Hubei Province

address: No.1 Shizishan Street, Hongshan District, Wuhan 430007, China

institute: Huazhong Agricultural University

summary: We reported the influence of disruption of the twin-arginine translocation system on the mRNA expression of the extra-intestinal pathogenic E. coli PCN033 strain.

overall_design: The cells of the extra-intestinal pathogenic E. coli PCN033 strain and the Tat system deleted strain were grown to the mid-log phase, and the mRNA was extracted and sequenced by illumina sequencing. The assay was performed in triplicate.


title: Influence of rYopM treatment on IMQ-induced psoriasiform dermatitis

city: Münster

first: Karin

last: Loser

address: Von-Esmarch-Str. 58

department: Experimental Dermatology

institute: University of Münster

summary: RNA-seq of skin of vehicle-treated, IMQ-treated, IMQ+rYopM-treated and IMQ+rYopM_LRR1-3 treated mice.

overall_design: Daily application of imiquimod (IMQ) or vehicle cream over 7 days. From beginning of disease additionally s.c. injection of PBS, recombinant Yersinia outer protein M (rYopM) or the truncated version rYopM_LRR1-3 until end of experiment on a daily basis. rYopM_LRR1-3 is a truncated version of rYopM containing only the two N-terminal alpha-helices and the first three leucine rich repeats (LRR) of the protein.

first: K

first: M

last: Schneeweiß


title: A chromatin immunoprecipitation database for prokarytic organisms [Escherichia coli]

address: 9500 Gilman Dr.

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Here, we present the genome-wide binding for major TFs in E. coli K-12 MG1655.

overall_design: Identification of genome-wide bindings for transcription factors in Escherichia coli K-12 MG1655 using ChIP-exo technology


title: Induction of trophoblast stem cells from human pluripotent stem cells [RNA-seq]

overall_design: We compared the transcriptome of  human trophoblast stem cells and human embryonic stem cells by RNA-Seq.


title: A chromatin immunoprecipitation database for prokarytic organisms [fur]

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of ferric uptake regulator (Fur) across gram-negative bacteria. Here, we present the genome-wide binding for Fur in multi-species.

sample_organism:
Escherichia coli
Klebsiella pneumoniae
Shigella flexneri
Yersinia pseudotuberculosis
Salmonella enterica

overall_design: Identification of genome-wide Fur bindings for transcription factors in multi-species using ChIP-exo technology


title: Transcriptome analysis of the kidney of obscure puffer Takifugu obscurus challenged with poly(I:C)

city: nanjing

first: ruixia

last: wang

address: xikang road

institute: hohai university

summary: Obscure puffer is an important aquaculture species in China, but the disease problem of this species seriously affects their production and causes huge economic losses. To reveal the molecular mechanisms of the disease resistance, Polyinosinic - polycytidylic acid poly(I:C) was used to stimulate obscure puffer. Kidneys were collected at 0, 12, and 48 h (To0, To12, and To48) for transcriptome de novo sequencing. This study obtained a large number of information resources on the transcriptome of obscure puffer, which can serve as a reference for further research on the immune regulation mechanisms of obscure puffer in the future.

first: Ruixia

last: Wang

first: Ying

first: Yan

last: Shi

first: Zhe

last: Zhao


title: RNA sequence between miR-155KONf1KO and Nf1KO

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: RNA sequence results between miR-155KONf1KO mouse tumor group (n=3) and Nf1KO mouse tumor group (n=3)

overall_design: We performed RNA sequence on miRR-155KONf1KO mouse tumor group (n=3) and Nf1KO mouse tumor group (n=3) to determine potential miR-155 targets by checking differential gene expression fold change

first: Youjin

first: Ashley

last: Hall

first: Jonathan

last: Rose

first: Jianqiang

last: Wu


title: A chromatin immunoprecipitation database for prokarytic organisms [salmonella]

first: Ye

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in Salmonella enterica Typhimurium LT2. Here, we present the genome-wide binding for YdcI in the Salmonella enterica Typhimurium LT2.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Identification of genome-wide bindings for transcription factors in Salmonella enterica Typhimurium LT2 using ChIP-exo technology

first: Bernhard


title: A chromatin immunoprecipitation database for prokarytic organisms [putida]

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in Pseudomonas putida. Here, we present the genome-wide binding for major TFs in P. putida.

overall_design: Identification of genome-wide bindings for transcription factors in Pseudomonas putida using ChIP-exo technology


title: A chromatin immunoprecipitation database for prokarytic organisms [multi_tf]

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in E. coli K-12 MG1655. Here, we present the genome-wide binding for dozens of major TFs and NAPs in the E. coli K-12 MG1655.

overall_design: Identification of genome-wide bindings for transcription factors in E. coli K-12 MG1655, using ChIP-exo technology


title: MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish

status: Public on Aug 14 2021

city: Nanjing

first: Wenshuang

last: Jia

address: NO.129 Jiangjun Road

institute: Nanjing University

summary: Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis, we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos (gata5/6 morphants) and control embryos.

overall_design: The embryos microinjected with control MO or gata5/6 MOs at 1-cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO, or 7.5 ng control MO per embryo.

first: Qingshun


title: Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken

city: Los Angeles

first: Gee-Way

last: Lin

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

summary: Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis. Retrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins 1) are often tuned up or down collectively as a sub-cluster, and 2) these changes occur in a temporo-spatial specific manner. This cluster-level suppression is also seen in MMPs on Chromosome 1. SATB2 alters gene expression changes of most other transcripts without this cluster-level switching. These results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.

overall_design: To understand the function of SATB2 in avian skin appendages during epidermal morphogenesis and differentiation, the avian retrovirus (RCAS) carrying a wild-type version of SATB2-OE was transfected in chick embryos at E3. Then RCAS-SATB2-OE transduced skin appendages including beaks, feathers and scales during the epidermal differentiation (E14 or E16) were collected for further RNA-seq analysis.

first: Yung-Chih

last: Lai

first: Ya-Chen

last: Liang

first: Ping

first: Cheng-Ming

last: Chuong


title: Whole-genome shRNA to identify sensitizers to MEK and IGF1R inhibitors

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: H23 cells were infected with a whole-genome shRNA library, treated with MEK and/or IGF1R inhibitors for 6 days. At the end of the treatment genomic DNA was extracted. PCR amplified and shRNAs inserts were quantified by NGS.

overall_design: shRNA screen in one lung cancer cell line treated with MEK and/or IGF1R inhibitors for 6 days

first: Molina-Arcas

last: Miriam

first: Horswell

last: Stuart

first: Downward

last: Julian


title: A chromatin immunoprecipitation database for prokarytic organisms [NAP]

last: Gao

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators and nucleoid associated proteins (NAPs) in E. coli K-12 MG1655. Here, we present the genome-wide binding for dozens of major TFs and NAPs in the E. coli K-12 MG1655.

overall_design: Identification of genome-wide bindings for nucleoid associated proteins in E. coli K-12 MG1655, using ChIP-exo technology

first: Donghyuk

last: Kim

last: Palsson


title: Mouse blood gene expression after administration of 137 Cesium

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
In the current study, we investigated the gene expression response of blood cells of mice that were injected with variable amounts of 137Cs
We isolated total RNA from peripheral blood from mice with 0 (control), 158, 191, 215 and 259 uCi cesium source amount on days 2, 3, 5, 7 and 14 days after injection. Using Agilent Mouse Whole Genome microarrays, we identified x genes that were significantly differentially expressed across the 14-day time course of this study. We identified common biological functions affected that persisted across the 14-day study.

overall_design: Radiation induced gene expression was measured at 2, 3, 5, 7 and 14 days after injection. There were a minimum of 6 replicates per group in this study.

first: Sally

last: Amundson


title: The stem cell transcription factor SOX2 is essential for astrocyte maturation and controls animal hyperactive behavior

city: Sacramento

first: Fuzheng

last: Guo

address: 2425 Stockton Blvd

institute: University of California Davis

summary: Children with SOX2-deficiency develop anophthalmia/microphthalmia and display neurological impairment. Here we report an essential role for astroglial SOX2 in brain anomalies and neurological defects. Sox2-deficiency inhibited postnatal astrocyte maturation without affecting astroglial proliferation and population expansion. Mechanistically, we found that SOX2 directly bound to a cohort of astrocytic signature genes such as those involving in glutamate transport and that Sox2-deficiency remarkably reduced glutamate transporter expression and compromised astrocyte function of glutamate uptake. Behaviorally, astroglial Sox2-deficient mice developed hyperactivity in locomotion while their motor skills, social capability, and learning abilities were unaffected. We found that astroglial Sox2-deficiency results in elevated glutamatergic synapse formation and elevated excitability of striatal medium spiny neurons, which has been shown to trigger hyperactive locomotion. Our study provides new insights into the biological mechanisms underlying brain defects in children with SOX2 mutations and unveils a novel connection between astrocyte SOX2 and brain development and behavior.

overall_design: Three astrocyte-specific Sox2 cKO adult mice (P80) carrying mGfap-Cre and Sox2fl/fl and three control adult mice (P80) carrying mGfap-Cre or Sox2fl/fl were used for harvesting the spinal cord. Total RNA was extracted for whole spinal cord and subjected to NGS RNA-seq

first: Sheng

last: Zhang


title: Application of Array CGH technique for the clinical diagnosis of developmental delay and congenital malformations in Saudi Arabia [400k]

status: Public on Aug 13 2021

city: Jeddah

first: Sajjad

last: Karim

state: Makka

address: Sulemania, CEGMR-80216

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

type: Genome variation profiling by genome tiling array

summary: Chromosomal imbalances are implicated in the etiology of developmental delay (DD) and congenital malformation (CM). We therefore conducted high resolution array comparative genomic hybridization (array CGH) of sixty three Saudi patients [11 by Agilent-001850/CGH1x244A and 52 by Agilent-014693/CGH2x400k] for investigating and understanding the genetic heterogeneity underlying DD/CM. A total of 76 disease associated copy number variants (CNVs) were detected in twenty four patients including 1p36, 1q21, 3p23, 6p24, 7q11, 8q24, 9q33, 10p14, 11p15, 11q12, 11q24, 13q21, 15q13, 16p13, 18q23, trisomy 18, 20q11, 21q22, 22q11.21, 47,XXY and 45,X0. The diagnosis rate of array CGH was 2.6 times higher than karyotyping.

overall_design: A total of 63 patients with developmental delay (DD) and congenital malformation (CM) were recruited for the study. Agilent Euro of homo sapines were used reference DNA [Male and Female: Part No 5190-3796 and 5190-3797].  To investigate genome defects, we applied high-density array CGH using SurePrint G3 Human CGH Microarray Kit, 1x244 K and 2x400 K, consisting of 244,000 and 400,000 copy number probes respectively (Agilent Technologies, Santa Clara, California, USA) using UCSC hg18 reference genome.

first: Karim

last: Sajjad

first: Hussein

last: Ibtessam

first: Alganmi

last: Nofe

first: Abusamra

last: Heba

first: Al-Attas

last: Manal

first: Chaudhary

last: Adeel

first: Al-Qahtani

last: Mohammed


title: Transcriptional profiling of wild-type (WT) and Ifnar1-SA (SA) in vitro differentiated Treg cells

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: Compared to wild-type (WT) Treg cells, Ifnar1-SA (SA) Treg cells have increased activity of IFN signaling pathways.

overall_design: RNA-seq of wild-type (WT) and Ifnar1-SA (SA) Treg cells that are induced from spleen naïve CD4 T cells in vitro.

first: Hongru

first: Serge

middle: Y

last: Fuchs


title: Microarray analysis to identify optimal timepoint post-ALVAC vaccintation to investigate innate immune pathways

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

institute: RPM Bioinfo Solutions

summary: ALVAC-Comp was an NHP immunogenicity study designed to identify the temporal kinetics of innate immune activation by ALVAC-SIV vaccination. PAXGENE tubes were harvested at 16h, 24h, 48h and 72h post vaccination to investigate the speed, magnitude, and durability of ALVAC-SIV induced innate immune activation. This study was set up to identify the optimal timepoint(s) post-vaccination in which to probe the cellular and molecular signaling mechanisms of innate immunity induced by vaccination.  Comparison of genes/pathways in common and unique to the 4 post-vaccination timepoints will reveal the order of innate immune induction post-vaccination.

overall_design: This NHP study of 6 animals consists of 4 vaccination timepoints. Two prime doses at Week 0 and 4 followed by two boost doses at Weeks 12 and 25. The prime consisted of ALVAC-SIV766Gag+SIV766gp120 and the boost consisted of 3 vaccines: A ALVAC-SIV766Gag+SIV766gp120, gD-766gp120 and gD-CG7Vgp120. PAXGENE tubes were taken at baseline (pre-Week 0) and at 16h, 24h, 48h and 72h post first boost. Sequential timepoints were used to identify the optimal timepoint post-vaccination to investigate innate immune function in based on modulation of gene expression patterns.

first: Namal

middle: M

last: Liyanage

first: Slim

last: Fourati

first: Genoveffa

last: Franchini


title: Substrate selectivity of semisynthetic Akt with pSer473 or O-GlcNAcSer473

city: Boston

first: Philip

last: Cole

address: 77 Avenue Louis Pasteur, 168 New Research Building

department: Department of Medicine

institute: Brigham and Womens Hospital

summary: Akt is a Ser/Thr protein kinase that regulates cell growth, metabolism and is considered a therapeutic target for cancer. Regulation of Akt by membrane recruitment and post-translational modifications (PTMs) has been extensively studied. The most well-established mechanism for cellular Akt activation involves phosphorylation on its activation loop on Thr308 by PDK1 and on its C-terminal tail on Ser473 by mTORC2. Other C-terminal tail PTMs have been identified, but their functional impacts have not been well-characterized. We use expressed protein ligation (EPL) as a tool to produce semisynthetic Akt proteins to dissect the enzymatic functions of these PTMs. We performed kinase assays employing human protein microarrays to investigate global substrate specificity of Akt, comparing phosphorylated vs. O-GlcNAcylated Ser473 forms.

overall_design: In this experiments, kinase assays were conducted for each semisynthetic Akt protein containing different modifications at the C-terminal tail: pSer473 and O-GlcNAcSer473. Controls were performed using all reaction components but leaving out Akt to leave out proteins capable of autophosphorylation. All experiments, including the control, were performed twice.

first: Antonieta

last: Salguero

first: Maggie

last: Chen

first: Aaron

last: Balana

first: Nam

last: Chu

first: Hanjie

last: Jiang

first: Katharine

last: Wright

first: Sara

last: Nathan

first: Sandra

middle: B

last: Gabelli

first: Matthew

last: Pratt


title: Cell intrinsic differences in human ALS motor neuron subtypes reveal a common disease mechanism and targeting lipid metabolites

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

summary: RNA-seq of differential vulnerability between human ocular and spinal motor neurons in ALS

overall_design: Transcriptional profiling of cultured human ocular and spinal motor neurons by RNA-Seq approaches

first: Gabsang

last: Lee

first: Hojae


title: Application of Array CGH technique for the clinical diagnosis of developmental delay and congenital malformations in Saudi Arabia [244k]

first: Sajjad

last: Karim

summary: Chromosomal imbalances are implicated in the etiology of developmental delay (DD) and congenital malformation (CM). We therefore conducted high resolution array comparative genomic hybridization (array CGH) of sixty three Saudi patients  [11 by Agilent-001850/CGH1x244A and 52 by Agilent-014693/CGH2x400k] for investigating and understanding the genetic heterogeneity underlying DD/CM. A total of 76 disease associated copy number variants (CNVs) were detected in twenty four patients including 1p36, 1q21, 3p23, 6p24, 7q11, 8q24, 9q33, 10p14, 11p15, 11q12, 11q24, 13q21, 15q13, 16p13, 18q23, trisomy 18, 20q11, 21q22, 22q11.21, 47,XXY and 45,X0. The diagnosis rate of array CGH was 2.4 times higher than karyotyping.

overall_design: A total of 63 patients with developmental delay (DD) and congenital malformation (CM) were recruited for the study. Agilent Euro of Homo sapiens were used reference DNA [Male and Female: Part No 5190-3796 and 5190-3797].  To investigate genome defects, we applied high-density array CGH using SurePrint G3 Human CGH Microarray Kit, 1x244 K and 2x400 K, consisting of 244,000 and 400,000 copy number probes respectively (Agilent Technologies, Santa Clara, California, USA) using UCSC hg18 reference genome. 11 samples.

first: Karim

last: Sajjad

first: Hussein

last: Ibtessam

first: Alganmi

last: Nofe

first: Abusamra

last: Heba

first: Al-Attas

last: Manal

first: Chaudhary

last: Adeel

first: Al-Qahtani

last: Mohammed


title: Single-cell profiling of tumor-infiltrating TCF7+ T cells reveals a T lymphocyte subset associated with tertiary lymphoid structures and superior prognosis in oral cancer

city: guangzhou

first: peng

last: yu

address: Department of Oral and Maxillofacial Surgery

institute: Sun Yat-sen Memorial Hospital of Sun Yat-sen University

summary: We isolated OSCC cells and performed single-cell RNA sequencing(scRNA-seq). Using immunohistochemistry(IHC) to analyze the relationship between TLS and prognosis. Multiple immunohistochemistry (MIHC), Flow cytometry (FCM) and Spatial analysis were used to verify the characteristics of TCF7+ T cells and their correlation with TLS. The prognostic significance, upstream regulatory network and intercellular communication of the TCF7+ T cell subpopulation were performed by multivariate analysis, Scenic and CellPhone software package analysis.We found a strong association between TCF7+ T cell subsets, TLSs and prognosis. The results suggested that TCF7+ T cells are expressing high levels of TLS-related genes and low levels of immune checkpoint molecules. Finally, we found that TCF7+ T cells were significantly associated with favorable outcomes. We also describe the upstream drivers and intercellular molecules that these cells rely on.The results showed that TCF7+ T cells could be used as a new therapeutic target to regulate the immune response of OSCC and are expected to be a new prognostic marker.

overall_design: Examination of 6 different OSCC patients

first: Jinsong

last: Li

first: Song

last: Fan

first: Yu

last: Peng